[BioC] affy( ) error with mas5()
Ying Chen
ying.chen at imclone.com
Wed Apr 9 16:21:39 CEST 2014
Hi guys,
I use affy to process over 3800 affy U133Plus2 arrays. rma() went well, but mas5() gave me the error during background correcting:
Error in matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), :
long vectors (argument 1) are not supported in .Fortran
I have been using affy() for a long time and this is the first time I run into such error. Any suggestion?
Thanks a lot for the help!
Ying
> data <- ReadAffy()
> eset <- mas5(data)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...
Error in matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), :
long vectors (argument 1) are not supported in .Fortran
> str(eset)
Error in str(eset) : object 'eset' not found
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
[7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] hgu133plus2cdf_2.13.0 AnnotationDbi_1.24.0 affy_1.40.0
[4] Biobase_2.22.0 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] affyio_1.30.0 BiocInstaller_1.12.0 DBI_0.2-7
[4] IRanges_1.20.7 preprocessCore_1.24.0 RSQLite_0.11.4
[7] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0
>
-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Abugri James
Sent: Wednesday, April 09, 2014 4:35 AM
To: bioconductor at r-project.org
Subject: [BioC] rehh package for iHS and Rsb
Dear Bioconductor community,
I have expressly read the manual and done the tutorial for the rehh package a dozen times, but still unable to apply it to my P. falciparum SNP data set. I have the SNP.INFO for P. falciparum. AND r scripts to call the genotypes and haplotypes. Has anybody got an experience in implementing this package.
--
*ABUGRI, James*
*Lecturer*
*Department of Applied Chemistry and Biochemistry* *Faculty of Applied Sciences* *University For Development Studies, Navrongo Campus* *Mobile; +233244994359 or +233204088294*
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